Staphylococcus aureus (S. aureus) is one of the most frequent causes of bacterial infections in the world. About 20% of the population is long-term carriers of S. aureus. S. aureus can cause a range of illnesses from minor skin infections, such as pimples, impetigo, boils, cellulitis folliculitis, furuncles, carbuncles, scalded skin syndrome and abscesses, to life-threatening diseases such as bacteraemia, pneumonia, meningitis, osteomyelitis, endocarditis, toxic shock syndrome (TSS), and septicaemia. Its incidence is from skin, soft tissue, respiratory, bone, joint, endovascular to wound infections. It is still one of the four most common causes of nosocomial infections, often causing postsurgical wound infections.
S. aureus may occur as a commensal on human skin; it also occurs in the nose frequently (in about a third of the population) and throat less commonly. Although the occurrence of S. aureus or MRSA under these circumstances does not indicate infection, healthy carriage of these bacteria is a major risk factor for infection, which usually manifests when normal barriers such as skin or mucosal lining have been breached. S. aureus can spread between individuals through direct contact with infected wounds, skin-to-skin contact, aerosol as well as by contact with contaminated objects such as towels, sheets, clothing, or athletic equipment. It can also colonize domestic animals such as pigs, cattle, dogs, cats and horses, and can cause various animal diseases such as mastitis in dairy cows and bumblefoot in chickens.
MRSA strains harbour the mecA gene, which confers resistance to all beta-lactam antibiotics and is often resistant to alternative antimicrobials (Chambers 1997). MRSA significantly contribute to mortality due to high risk of treatment failure, and results in an economical burden to the society due to prolonged hospitalization and recourse to more expensive antimicrobials. MRSA was originally confined to hospital and health care environments but during the last decade the incidence of community-acquired infections has increased.
Recently, MRSA belonging to a specific genetic lineage called CC398 has emerged in pigs, calves and other animals worldwide. MRSA CC398 colonizes the skin and the mucosal surfaces of healthy animals without any clinical signs. However, the emergence of this MRSA clone in animals represents a major public health problem since animal carriers may contribute to the spread of MRSA among humans. Independent studies in North America (Hanselmann et al. 2006), Holland (Wulf et al. 2006) and Denmark (Moodley et al. 2008; Wulf et al. 2008) have indicated the frequency of MRSA colonization is higher in veterinary staff and pig farmers than in the community. Two case-control studies in the Netherlands (van Loo et al. 2007) and in Denmark (Lewis et al. 2008) have shown that pig farmers are categories at risk for MRSA CC398 infection. Differently from other MRSA lineages, MRSA CC398 is likely to have animal origin and therefore is presently regarded as a zoonosis. It has been reported that the prevalence of MRSA among pig farmers was >760 times higher than that among patients admitted to Dutch hospitals (Voss et al. 2005). Typing of these MRSA indicated that they belonged to CC398 and had been transmitted from pigs to farm workers.
Recently it was established that CC398 accounted for 20% of all MRSA detected in the Netherlands (van Loo et al. 2007), highlighting the need for a fast, simple, inexpensive and reliable typing of this particular MRSA lineage. More generally, molecular typing of MRSA, in particular in hospital-acquired infections, is an important prerequisite for an effective and targeted use of infection control measures aimed at preventing further dissemination within hospitals as well as from the community to hospitals. In doing so, it is necessary to identify genetic markers allowing rapid and reliable MRSA identification at the CC level and easy communication of results between laboratories.
MRSA CC398 and more broadly any MRSA clones are currently identified using a multi-step procedure which includes: i) identification of S. aureus at the species level (Bannerman 2003); ii) detection of methicillin resistance by phenotypic and/or genotypic methods; and iii) clone identification using standard methods for S. aureus typing, namely pulsed-field gel electrophoresis (PFGE) (Murchan et al. 2003), multi-locus sequence typing (MLST) (Enright et al. 2000) and spa typing (Koreen et al. 2004). There have been attempts to merge the first two steps (Vannuffel et al. 1996). However, prior to the invention, no methods were available to cover all three steps. Recently, an restriction-modification (RM) system of S. aureus was described by Waldron et al. (2006). The RM system is composed by five genes: two hsdM (modification) genes, one hsdR (restriction) gene and two hsdS (specificity) genes. The two sau1hsdS genes (sau1hsdS1 and sau1hsdS2) were found to exhibit high sequence variation between isolates belonging to distinct CCs. This finding was subsequently used by Cockfield et al. (2008) to identify six distinct lineages (CC1, CC5, CC8, CC22, CC30 and CC45).
Due to the emerging importance of CC398 in the veterinary sector, the need for rapid methods for MRSA identification at the CC level is no longer limited to human medicine but is now extended to MRSA surveillance in living animals, farm environments and animal food products. In 2007 the EU Commission financed baseline surveys to assess the prevalence of MRSA in breeding pigs (EU Commission 2007). The EU initiative has been accompanied by a number of research and surveillance programs at the national level. This situation has determined a need for a specific method enabling rapid and accurate identification of CC398, including both MRSA and Methicillin-Sensitive S. aureus (MSSA) variants belonging to this S. aureus lineage. Therefore, the invention described herein below has important diagnostic and epidemiological applications in human medicine as well as in the veterinary sector. The invention represents a useful tool for surveillance and control of MRSA CC398 in humans, animals and food products, and more importantly, can be used for clone identification of any MRSA.